Prior Enrichment Research Articles

Nanopore sequencing: An enrichment-free alternative to mitochondrial DNA sequencing.

Mitochondrial DNA sequence data are often utilized in disease studies, conservation genetics and forensic identification. The current approaches for sequencing the full mtGenome typically require several rounds of PCR enrichment during Sanger or MPS protocols followed by fairly tedious assembly and analysis. Here we describe an efficient approach to sequencing directly from genomic DNA samples without prior enrichment or extensive library preparation steps. A comparison is made between libraries sequenced directly from native DNA and the same samples sequenced from libraries generated with nine overlapping mtDNA amplicons on the Oxford Nanopore MinION™ device. The native and amplicon library preparation methods and alternative base calling strategies were assessed to establish error rates and identify trends of discordance between the two library preparation approaches. For the complete mtGenome, 16 569 nucleotides, an overall error rate of approximately 1.00% was observed. As expected with mtDNA, the majority of error was detected in homopolymeric regions. The use of a modified basecaller that corrects for ambiguous signal in homopolymeric stretches reduced the error rate for both library preparation methods to approximately 0.30%. Our study indicates that direct mtDNA sequencing from native DNA on the MinION™ device provides comparable results to those obtained from common mtDNA sequencing methods and is a reliable alternative to approaches using PCR‐enriched libraries.

Evaluation of consensus method for the culture of Burkholderia pseudomallei in soil samples from Laos.

Background: We have previously shown that PCR following enrichment culture is the most sensitive method to detect Burkholderia pseudomallei in environmental samples. Here we report an evaluation of the published consensus method for the culture of B. pseudomallei from Lao soil in comparison with our conventional culture method and with PCR with or without prior broth enrichment. Methods: One hundred soil samples were collected from a field known to contain B. pseudomallei and processed by: (i) the conventional method, (ii-iii) the consensus method using media prepared in either Laos or Thailand, and (iv) the consensus method performed in Thailand, as well as by (v) PCR following direct extraction of DNA from soil and (vi) PCR following broth pre-enrichment. Results: The numbers of samples in which B. pseudomallei was detected were 42, 10, 7, 6, 6 and 84, respectively. However, two samples were positive by the consensus method but negative by conventional culture, and one sample was negative by PCR following enrichment although B. pseudomallei was isolated by the conventional culture method. Conclusions/Discussion: The results show that no single method will detect all environmental samples that contain B. pseudomallei. People conducting environmental surveys for this organism should be aware of the possibility of false-negative results using the consensus culture method. An approach that entails screening using PCR after enrichment, followed by the evaluation of a range of different culture methods on PCR-positive samples to determine which works best in each setting, is recommended.

Evaluation of consensus method for the culture of Burkholderia pseudomallei in soil samples from Laos

Background: We have previously shown that PCR following enrichment culture is the most sensitive method to detect Burkholderia pseudomallei in environmental samples. Here we report an evaluation of the published consensus method for the culture of B. pseudomallei from Lao soil in comparison with our conventional culture method and with PCR with or without prior broth enrichment. Methods: One hundred soil samples were collected from a field known to contain B. pseudomallei and processed by: (i) the conventional method, (ii-iii) the consensus method using media prepared in either Laos or Thailand, and (iv) the consensus method performed in Thailand, as well as by (v) PCR following direct extraction of DNA from soil and (vi) PCR following broth pre-enrichment. Results: The numbers of samples in which B. pseudomallei was detected were 42, 10, 7, 6, 6 and 84, respectively. However, two samples were positive by the consensus method but negative by conventional culture, and one sample was negative by PCR following enrichment although B. pseudomallei was isolated by the conventional culture method. Conclusions/Discussion: The results show that no single method will detect all environmental samples that contain B. pseudomallei. People conducting environmental surveys for this organism should be aware of the possibility of false-negative results using the consensus culture method. An approach that entails screening using PCR after enrichment, followed by the evaluation of a range of different culture methods on PCR-positive samples to determine which works best in each setting, is recommended.

T5 Exonuclease Hydrolysis of Hepatitis B Virus Replicative Intermediates Allows Reliable Quantification and Fast Drug Efficacy Testing of Covalently Closed Circular DNA by PCR.

Chronic infection with the human hepatitis B virus (HBV) is a major health problem. Virus persistence requires the establishment and maintenance of covalently closed circular DNA (cccDNA), the episomal virus template in the nucleus of infected hepatocytes. Compared to replicative DNA intermediates (relaxed circular DNA [rcDNA]), copy numbers of cccDNA in infected hepatocytes are low. Accordingly, accurate analyses of cccDNA require enrichment of nuclear fractions and Southern blotting or selective quantitative PCR (qPCR) methods allowing discrimination of cccDNA and rcDNA. In this report, we analyzed cccDNA-specific primer pairs for their ability to amplify cccDNA selectively. Using mixtures of defined forms of HBV and genomic DNA, we determined the potential of different nucleases for targeted digestion of the open/relaxed circular DNA forms in the absence and presence of genomic DNA without affecting cccDNA. We found that the combination of T5 exonuclease with a primer set amplifying an approximately 1-kb fragment permits reliable quantification of cccDNA without the requirement of prior nucleus enrichment or Hirt extraction. We tested this method in four different in vitro infection systems and quantified cccDNA copy numbers at increasing multiplicities of inoculated genome equivalents. We further analyzed the kinetics of cccDNA formation and the effect of drugs (interferon, entry inhibitors, and capsid inhibitors) on cccDNA. Our method allows reliable cccDNA quantification at early stages of infection in the presence of a high excess of input virus and replicative intermediates and is thereby suitable for drug screening and investigation of cccDNA formation and maintenance.IMPORTANCE cccDNA elimination is a major goal in future curative regimens for chronic HBV patients. However, PCR-based assays for cccDNA quantification show a principally constrained specificity when high levels of input virus or replicative intermediates are present. Here, we characterized T5 exonuclease as a suitable enzyme for medium-throughput in vitro assays that preserves cccDNA but efficiently removes rcDNA prior to PCR-based quantification. We compared T5 exonuclease with the previously described exonuclease III and showed that both nucleases are suitable for reliable quantification of cccDNA by PCR. We substantiated the applicability of our method through examination of early cccDNA formation and stable accumulation in several in vitro infection models and analyzed cccDNA stability after administration of anti-HBV drugs. Our results support the use of T5 exonuclease for fast and convenient rcDNA removal, especially for early cccDNA quantification and rapid drug testing in in vitro studies.

Evaluation of consensus method for the culture of Burkholderia pseudomallei in soil samples from Laos

Background: We have previously shown that PCR following enrichment culture is the most sensitive method to detect Burkholderia pseudomallei in environmental samples. Here we report an evaluation of the published consensus method for the culture of B. pseudomallei from Lao soil in comparison with our conventional culture method and with PCR with or without prior broth enrichment. Methods: One hundred soil samples were collected from a field known to contain B. pseudomallei and processed by: (i) the conventional method, (ii-iii) the consensus method using media prepared in either Laos or Thailand, and (iv) the consensus method performed in Thailand, as well as by (v) PCR following direct extraction of DNA from soil and (vi) PCR following broth pre-enrichment. Results: The numbers of samples in which B. pseudomallei was detected were 42, 10, 7, 6, 6 and 84, respectively. However, two samples were positive by the consensus method but negative by conventional culture, and one sample was negative by PCR following enrichment although B. pseudomallei was isolated by the conventional culture method. Conclusions/Discussion: The results show that no single method will detect all environmental samples that contain B. pseudomallei. People conducting environmental surveys for this organism should be aware of the possibility of false-negative results using the consensus culture method. An approach that entails screening using PCR after enrichment, followed by the evaluation of a range of different culture methods on PCR-positive samples to determine which works best in each setting, is recommended.

P3.03-20 Circulating Tumor Cell Clustering in Vitro Short-Term Culture Correlates with Poor Survival and Allows Monitoring Response to Treatment

Circulating tumor cells (CTCs) are putative markers for tumor prognosis and may serve to evaluate patient’s response to chemotherapy. CTCs are often detected as single cells but infrequently as clusters indicative of worse prognosis. Blood samples were obtained from the 86 breast cancer patients, 52 lung cancer patients. The nucleated cells were cultured in ellipsoidal microwells The microwells were prepared by placing a cover slip (22mm X 22mm) on a 35mm culture dish. Molten agar (3%) was poured on the top of the cover slip enough to cover it (500μl approx). The ellipsoidal microwell in PDMS (polydimethylsiloxane) was then placed on the top of the cover slip containing the molten agar and allowed it to solidify. The culture conditions were carried at 37°C, 5% CO2 and humidified hypoxic conditions (1% O2). The culture medium was replaced every 48-72 hrs with nominal disturbances to the microwells. Cultures were maintained for 3 weeks and imaged on day 7, 14, 21 with bright field microscope and analyzed the images using (Olympus IX71). To correlate cluster formation with survival, samples were obtained from 31 patients with lung cancer. These patients were enrolled, when they were presented with progressive disease since their last treatment regimen but before commencing a new treatment regimen. Blood was collected before and on 9th, 12th week after the treatment. It is interesting to note that tight cluster formation correlated with patient survival. The Kaplan-Meier survival analysis showed that cluster formation in patients who have undergone neoadjuvant therapy correlated with shorter overall survival Our culture system enabled us to successfully expand the CTCs without any prior enrichment. The method requires 2.5 ml of blood per 35-mm dish to expand CTCs. Microwells were easy to establish and replicate with minimal set-up in a laboratory. To the best of our knowledge, this study is one of the few, which suggest the possible role of cluster formation in patient survival in Lung cancer patients.

The clinical heterogeneity of preeclampsia is related to both placental gene expression and placental histopathology

Preeclampsia is a life-threatening disorder of pregnancy, demonstrating a high degree of heterogeneity in clinical features such as presentation, disease severity, and outcomes. This heterogeneity suggests distinct pathophysiological mechanisms may be driving the placental disease underlying this disorder. Our group recently reported distinct clusters of placental gene expression in preeclampsia and control pregnancies, allowing for the identification of at least 3 clinically relevant gene expression-based subtypes of preeclampsia. Histopathological examination of a small number of samples from 2 of the gene expression-based subtypes revealed placental lesions consistent with their gene expression phenotype, suggesting that detailed placental histopathology may provide further insight into the pathophysiology underlying these distinct gene expression-based subtypes. The objective of the study was to assess histopathological lesions in the placentas of patients belonging to each identified gene expression-based subtype of preeclampsia, characterized in our previous study. Our goal was to further understand the pathophysiologies defining these gene expression-based subtypes by integrating gene expression with histopathological findings, possibly identifying additional subgroups of preeclampsia patients. Paraffin-embedded placental biopsies from patients included in the gene expression profiling study (n= 142 of 157, 90.4%) were sectioned, hematoxylin and eosin stained, and imaged. An experienced perinatal pathologist, blinded to gene expression findings and clinical information, assessed the presence and severity of histological lesions using a comprehensive, standardized data collection form. The frequency and severity scores of observed histopathological lesions were compared among gene expression-based subtypes as well as within each subtype using using Fisher exact tests, Kruskal-Wallis tests, and hierarchical clustering. The histological findings of the placental samples were visualized using t-distributed stochastic neighbor embedding and phylogenetic trees. Concordance and discordance between gene expression findings and histopathology were also investigated and visualized using principal component analysis. Several histological lesions were found to be characteristic of each gene expression-based preeclampsia subtype. The overall concordance between gene expression and histopathology for all samples was 65% (93 of 142), with characteristic placental lesions for each gene expression-based subtype complementing prior gene enrichment findings (ie, placentas with enrichment of hypoxia-associated genes showed severe lesions of maternal vascular malperfusion). Concordant samples were located in the central area of each gene expression-based cluster when viewed on a principal component analysis plot. Interestingly, discordant samples (gene expression and histopathology not reflective of one another) were generally found to lie at the periphery of the gene expression-based clusters and tended to border the group of patients with phenotypically similar histopathology. Our findings demonstrates a high degree of concordance between placental lesions and gene expression across subtypes of preeclampsia. Additionally, novel integrative analysis of scored placental histopathology severity and gene expression findings allowed for the identification of patients with intermediate phenotypes of preeclampsia not apparent through gene expression profiling alone. Future investigations should examine the temporal relationship between these 2 modalities as well as consider the maternal and fetal contributions to these subtypes of disease.

Unrestrictive identification of post-translational modifications in Hevea brasiliensis latex.

The natural rubber latex extracted from the bark of Hevea brasiliensis plays various important roles in modern society. Post-translational modifications (PTMs) of the latex proteins are important for the stability and functionality of the proteins. In this study, latex proteins were acquired from the C-serum, lutoids, and rubber particle layers of latex without using prior enrichment steps; they were fragmented using collision-induced dissociation (CID), higher-energy collisional dissociation (HCD), and electron-transfer dissociation (ETD) activation methods. PEAKS 7 were used to search for unspecified PTMs, followed by analysis through PTM prediction tools to crosscheck both results. There were 73 peptides in 47 proteins from H. brasiliensis protein sequences derived from UniProtKB were identified and predicted to be post-translationally modified. The peptides with PTMs identified include phosphorylation, lysine acetylation, N-terminal acetylation, hydroxylation, and ubiquitination. Most of the PTMs discovered have yet to be reported in UniProt, which would provide great assistance in the research of the functional properties of H. brasiliensis latex proteins, as well as being useful biomarkers. The data are available via the MassIVE repository with identifier MSV000082419.

Rapid Detection of Escherichia coli O157:H7 in Fresh Lettuce Based on Localized Surface Plasmon Resonance Combined with Immunomagnetic Separation

This study presents a method for rapid detection of Escherichia coli O157:H7 in fresh lettuce based on the properties of target separation and localized surface plasmon resonance of immunomagnetic nanoparticles. The multifunctional immunomagnetic nanoparticles enabling simultaneous separation and detection were prepared by synthesizing magnetic nanoparticles (ca. 10 nm in diameter) composed of an iron oxide (Fe3O4) core and gold shell and then conjugating these nanoparticles with the anti- E. coli O157:H7 antibodies. The application of multifunctional immunomagnetic nanoparticles for detecting E. coli O157:H7 in a lettuce matrix allowed detection of the presence of <1 log CFU mL-1 without prior enrichment. In contrast, the detection limit of the conventional plating method was 2.74 log CFU mL-1. The method, which requires no preenrichment, provides an alternative to conventional microbiological detection methods and can be used as a rapid screening tool for a large number of food samples.

Characterization of product-related low molecular weight impurities in therapeutic monoclonal antibodies using hydrophilic interaction chromatography coupled with mass spectrometry

Traditional SDS-PAGE method and its modern equivalent CE-SDS method are both widely applied to assess the purity of therapeutic monoclonal antibody (mAb) drug products. However, structural identification of low molecular weight (LMW) impurities using those methods has been challenging and largely based on empirical knowledges. In this paper, we present that hydrophilic interaction chromatography (HILIC) coupled with mass spectrometry analysis is a novel and orthogonal method to characterize such LMW impurities present within a purified mAb drug product sample. We show here that after removal of N-linked glycans, the HILIC method separates mAb-related LMW impurities with a size-based elution order. The subsequent mass measurement from a high-resolution accurate mass spectrometer provides direct and unambiguous identification of a variety of low-abundance LMW impurities within a single LC–MS analysis. Free light chain, half antibody, H2L species (antibody possessing a single light chain) and protein backbone-truncated species can all be confidently identified and elucidated in great detail, including the truncation sites and associated post-translational modifications. It is worth noting that this study provides the first example where the H2L species can be directly detected in a mAb drug product sample by intact mass analysis without prior enrichment.

Molecular transitions in early progenitors during human cord blood hematopoiesis

Hematopoietic stem cells (HSCs) give rise to diverse cell types in the blood system, yet our molecular understanding of the early trajectories that generate this enormous diversity in humans remains incomplete. Here, we leverage Drop‐seq, a massively parallel single‐cell RNA sequencing (scRNA‐seq) approach, to individually profile 20,000 progenitor cells from human cord blood, without prior enrichment or depletion for individual lineages based on surface markers. Our data reveal a transcriptional compendium of progenitor states in human cord blood, representing four committed lineages downstream from HSC, alongside the transcriptional dynamics underlying fate commitment. We identify intermediate stages that simultaneously co‐express “primed” programs for multiple downstream lineages, and also observe striking heterogeneity in the early molecular transitions between myeloid subsets. Integrating our data with a recently published scRNA‐seq dataset from human bone marrow, we illustrate the molecular similarity between these two commonly used systems and further explore the chromatin dynamics of “primed” transcriptional programs based on ATAC‐seq. Finally, we demonstrate that Drop‐seq data can be utilized to identify new heterogeneous surface markers of cell state that correlate with functional output.

SWATH mass spectrometry as a tool for quantitative profiling of the matrisome

Proteomic analysis of extracellular matrix (ECM) and ECM-associated proteins, collectively known as the matrisome, is a challenging task due to the inherent complexity and insolubility of these proteins. Here we present sequential window acquisition of all theoretical fragment ion spectra mass spectrometry (SWATH MS) as a tool for the quantitative analysis of matrisomal proteins in both non-enriched and ECM enriched tissue without the need for prior fractionation. Utilising a spectral library containing 201 matrisomal proteins, we compared the performance and reproducibility of SWATH MS over conventional data-dependent analysis mass spectrometry (DDA MS) in unfractionated murine lung and liver. SWATH MS conferred a 15–20% increase in reproducible peptide identification across replicate experiments in both tissue types and identified 54% more matrisomal proteins in the liver versus DDA MS. We further use SWATH MS to evaluate the quantitative changes in matrisome content that accompanies ECM enrichment. Our data shows that ECM enrichment led to a systematic increase in core matrisomal proteins but resulted in significant losses in matrisome-associated proteins including the cathepsins and proteins of the S100 family. Our proof-of-principle study demonstrates the utility of SWATH MS as a versatile tool for in-depth characterisation of the matrisome in unfractionated and non-enriched tissues. SignificanceThe matrisome is a complex network of extracellular matrix (ECM) and ECM-associated proteins that provides scaffolding function to tissues and plays important roles in the regulation of fundamental cellular processes. However, due to its inherent complexity and insolubility, proteomic studies of the matrisome typically require the application of enrichment workflows prior to MS analysis. Such enrichment strategies often lead to losses in soluble matrisome-associated components. In this study, we present sequential window acquisition of all theoretical fragment ion spectra mass spectrometry (SWATH MS) as a tool for the quantitative analysis of matrisomal proteins. We show that SWATH MS provides a more reproducible coverage of the matrisome compared to data-dependent analysis (DDA) MS. We also demonstrate that SWATH MS is capable of accurate quantification of matrisomal proteins without prior ECM enrichment and fractionation, which may simplify sample handling workflows and avoid losses in matrisome-associated proteins commonly linked to ECM enrichment.

Immunocontraceptive target repertoire defined by systematic identification of sperm membrane alloantigens in a single species.

Sperm competence in animal fertilization requires the collective activities of numerous sperm-specific proteins that are typically alloimmunogenic in females. Consequently, sperm membrane alloantigens are potential targets for contraceptives that act by blocking the proteins’ functions in gamete interactions. Here we used a targeted proteomics approach to identify the major alloantigens in swine sperm membranes and lipid rafts, and thereby systematically defined the repertoire of these sperm-specific proteins in a single species. Gilts with high alloantibody reactivity to proteins in sperm membranes or lipid rafts produced fewer offspring (73% decrease) than adjuvant-only or nonimmune control animals. Alloantisera recognized more than 20 potentially unique sperm membrane proteins and five sperm lipid raft proteins resolved on two-dimensional immunoblots with or without prior enrichment by anion exchange chromatography. Dominant sperm membrane alloantigens identified by mass spectrometry included the ADAMs fertilin α, fertilin ß, and cyritestin. Less abundant alloantigens included ATP synthase F1 β subunit, myo-inositol monophosphatase-1, and zymogen granule membrane glycoprotein-2. Immunodominant sperm lipid raft alloantigens included SAMP14, lymphocyte antigen 6K, and the epididymal sperm protein E12. Of the fifteen unique membrane alloantigens identified, eleven were known sperm-specific proteins with uncertain functions in fertilization, and four were not previously suspected to exist as sperm-specific isoforms. De novo sequences of tryptic peptides from sperm membrane alloantigen “M6” displayed no evident homology to known proteins, so is a newly discovered sperm-specific gene product in swine. We conclude that alloimmunizing gilts with sperm membranes or lipid rafts evokes formation of antibodies to a relatively small number of dominant alloantigens that include known and novel sperm-specific proteins with possible functions in fertilization and potential utility as targets for immunocontraception.

Evaluation of an Accelerated Workflow for Surveillance of ESBL (CTX-M)-Producing Escherichia coli Using Amplicon-Based Next-Generation Sequencing and Automated Analysis.

Outbreak management of extended spectrum β-lactamase (ESBL)-producing pathogens requires rapid and accurate diagnosis. However, conventional screening is slow and labor-intensive. The vast majority of the screened samples are negative and detection of non-outbreak-related resistant micro-organisms often complicates outbreak management. In a CTX-M-15-producing Escherichia coli outbreak, 149 fecal samples and rectal eSwabs were collected by a cross-sectional survey in a Dutch nursing home. Samples were processed by routine diagnostic methods. Retrospectively, ESBL-producing bacteria and resistance genes were detected directly from eSwab medium by an accelerated workflow without prior enrichment cultures by an amplicon-based next-generation sequencing (NGS) method, and culture. A total of 27 (18.1%) samples were positive in either test. Sensitivity for CTX-M detection was 96.3% for the phenotypic method and 85.2% for the NGS method, and the specificity was 100% for both methods, as confirmed by micro-array. This resulted in a positive predictive value (PPV) of 100% for both methods, and a negative predictive value (NPV) of 99.2% and 96.8% for the phenotypic method and the NGS method, respectively. Time to result was four days and 14 h for the phenotypic method and the NGS method, respectively. In conclusion, the sensitivity without enrichment shows promising results for further use of amplicon-based NGS for screening during outbreaks.

A simple centrifugation protocol for metagenomic studies increases mitochondrial DNA yield by two orders of magnitude

Abstract DNA (meta)barcoding is applied to study biodiversity and is available for standardized biodiversity assessments. However, it suffers from PCR bias, which can lead to the loss of specific taxa. PCR‐free techniques such as shotgun metagenomics are therefore thought to be more suited for biodiversity assessments, but are currently limited by incomplete reference libraries. The technique of “mitogenome‐skimming” or “mitogenomics,” in which complete mitochondrial genomes are sequenced, is ideal to bridge the techniques of (meta)barcoding and metagenomics. However, without the enrichment of mitochondria, roughly 99% of all sequencing reads are of non‐mitochondrial origin and mostly useless for common applications, e.g. species identification. Here, we present a simple centrifugation protocol that leads to an average 140‐fold enrichment of mitochondrial DNA. By sequencing six ‘mock’‐communities—comprising the freshwater taxa Corbicula fluminea, Gammarus roeselii and Hydropsyche exocellata each—we recovered whole mitochondrial genomes of these species and the acanthocephalan endoparasite Pomphorhynchus laevis. The enrichment protocol will speed up building reference libraries for whole mitochondrial genomes, as dozens of species can be sequenced on a single MiSeq run. Subsequently, it will also allow biodiversity assessments, using mitogenomics at greatly reduced costs in comparison to mitogenomic approaches without prior enrichment for mitochondria.

Expansion of patient-derived circulating tumor cells from liquid biopsies using a CTC microfluidic culture device.

The development of personalized cancer therapy depends on a robust system to monitor the patient's individual response to anticancer treatment. Anticancer drug efficacy has been tested on circulating tumor cells (CTCs) derived from patient blood samples after ex vivo expansion into CTC clusters. Current attempts to culture these primary cancer cells focus on long-term maintenance under growth factor supplements into cell lines, which usually takes >6 months and results in a CTC expansion efficiency of <20%. We recently developed a simple but unique microfluidics-based culture approach that requires minimal preprocessing (∼30 min) and does not require prior enrichment of CTCs or depend on the use of growth factor supplements. The approach capitalizes on co-culture of immune cells from the same patient blood sample within specially designed microwells that promote CTC cluster formation within 2 weeks, with an overall cluster formation success rate of ∼50%. Drug screening is facilitated by the incorporation of a gradient generator for parallel exposure to two or more drugs at various concentrations. Owing to the cost-effectiveness and less-invasive nature of this procedure, routine monitoring of disease progression can be achieved. The described microfluidics system can be operated with a single syringe pump to introduce drug compounds (which takes ∼6 min), followed by incubation of the CTC clusters for 48 h before analysis. In addition to its applications in biomedical research, the rapid readout of our platform will enable clinicians to assess or predict a patient's response to various therapeutic strategies, so as to enable personalized or precision therapy.

Integrated Bayesian analysis of rare exonic variants to identify risk genes for schizophrenia and neurodevelopmental disorders

BackgroundIntegrating rare variation from trio family and case–control studies has successfully implicated specific genes contributing to risk of neurodevelopmental disorders (NDDs) including autism spectrum disorders (ASD), intellectual disability (ID), developmental disorders (DDs), and epilepsy (EPI). For schizophrenia (SCZ), however, while sets of genes have been implicated through the study of rare variation, only two risk genes have been identified.MethodsWe used hierarchical Bayesian modeling of rare-variant genetic architecture to estimate mean effect sizes and risk-gene proportions, analyzing the largest available collection of whole exome sequence data for SCZ (1,077 trios, 6,699 cases, and 13,028 controls), and data for four NDDs (ASD, ID, DD, and EPI; total 10,792 trios, and 4,058 cases and controls).ResultsFor SCZ, we estimate there are 1,551 risk genes. There are more risk genes and they have weaker effects than for NDDs. We provide power analyses to predict the number of risk-gene discoveries as more data become available. We confirm and augment prior risk gene and gene set enrichment results for SCZ and NDDs. In particular, we detected 98 new DD risk genes at FDR < 0.05. Correlations of risk-gene posterior probabilities are high across four NDDs (ρ>0.55), but low between SCZ and the NDDs (ρ<0.3). An in-depth analysis of 288 NDD genes shows there is highly significant protein–protein interaction (PPI) network connectivity, and functionally distinct PPI subnetworks based on pathway enrichment, single-cell RNA-seq cell types, and multi-region developmental brain RNA-seq.ConclusionsWe have extended a pipeline used in ASD studies and applied it to infer rare genetic parameters for SCZ and four NDDs (https://github.com/hoangtn/extTADA). We find many new DD risk genes, supported by gene set enrichment and PPI network connectivity analyses. We find greater similarity among NDDs than between NDDs and SCZ. NDD gene subnetworks are implicated in postnatally expressed presynaptic and postsynaptic genes, and for transcriptional and post-transcriptional gene regulation in prenatal neural progenitor and stem cells.

Detection of Listeria monocytogenes based on combined aptamers magnetic capture and loop-mediated isothermal amplification

Rapid detection of Listeria monocytogenes (L. monocytogenes) is important to ensure timely treatment and to prevent outbreaks of listeriosis. Here, we reported an efficient and accurate system using aptamers magnetic capture and loop-mediated isothermal amplification (AMC-LAMP) for sensitive detection of L. monocytogenes. A set of combined aptamers (including four individual aptamers with high binding affinity to L. monocytogenes) was conjugated to magnetic beads, used for capture L. monocytogenes. After incubation at room temperature for 45 min, the captured L. monocytogenes cells were directly used for DNA extraction (1 h). Subsequently, the LAMP assays were carried out at 63 °C for 40 min, and the amplification products were visualized via SYBR Green® I staining. The AMC-LAMP had a detection limit of 5 CFU/mL, and the total assay time was approximate 3 h. By the protocols developed in this study, 17 food samples was test for L. monocytogenes without prior culture enrichment. The accuracy of AMC-LAMP was shown to be 100% when compared with culture-biotechnical examination, while PCR failed to detect L. monocytogenes in one of five positive samples. These results indicate the developed AMC-LAMP is a potential useful method for rapid screening and on-site detection of L. monocytogenes in food samples.

LC–MS/MS Method for Simultaneous Determination of Monoethanol- and Dimethylnitramine in Aqueous Soil Extracts

Monoethanol (MEA)- and dimethyl (DMA)-nitramines are by-products of amine-based post-combustion CO2 capture (PCCC) processing, and are potentially carcinogenic. The compounds are challenging to measure, also with LC–tandem mass spectrometry (MS/MS), attributed to their high polarity and extreme proneness to matrix effects. In contrast to related methods, the MEA- and DMA-nitramines were simultaneously determined in aqueous soil extracts in less than 10 min using a 1 mm × 150 mm Atlantis® T3 (3 µm) C18 column. A mobile phase of water/methanol (90/10, v/v) and 2 mM acetic acid allowed for electrospray ionization (ESI) of both analytes [in contrast to the need for both ESI and atmospheric pressure chemical ionization (APCI) in related methods]. Polarity switching electrospray was required for the simultaneous detection of the analytes, and concentration limits of detection (LODs) in the aqueous soil extracts were ≤5.0 µg L−1 using an injection volume of 20 μL and no prior enrichment step. Matrix effects were compensated for using isotope-labelled internal standards, and satisfactory precision and linearity were obtained (within- and between-day precisions ≤19%, r 2 ≥ 0.995 for concentrations up to 500.0 µg L−1). To avoid signal decrease over time when measuring DMA-nitramine alone, the use of polarity switching was beneficial, in addition to frequent cleaning of the ion transfer capillary. The validated method can be used to determine nitramines in aqueous soil extracts, which is of importance as soil sorption is a determinant of the compounds’ environmental fate.

Lost in plasmids: next generation sequencing and the complex genome of the tick-borne pathogen Borrelia burgdorferi

BackgroundBorrelia (B.) burgdorferi sensu lato, including the tick-transmitted agents of human Lyme borreliosis, have particularly complex genomes, consisting of a linear main chromosome and numerous linear and circular plasmids. The number and structure of plasmids is variable even in strains within a single genospecies. Genes on these plasmids are known to play essential roles in virulence and pathogenicity as well as host and vector associations. For this reason, it is essential to explore methods for rapid and reliable characterisation of molecular level changes on plasmids.In this study we used three strains: a low passage isolate of B. burgdorferi sensu stricto strain B31(−NRZ) and two closely related strains (PAli and PAbe) that were isolated from human patients. Sequences of these strains were compared to the previously sequenced reference strain B31 (available in GenBank) to obtain proof-of-principle information on the suitability of next generation sequencing (NGS) library construction and sequencing methods on the assembly of bacterial plasmids. We tested the effectiveness of different short read assemblers on Illumina sequences, and of long read generation methods on sequence data from Pacific Bioscience single-molecule real-time (SMRT) and nanopore (Oxford Nanopore Technologies) sequencing technology.ResultsInclusion of mate pair library reads improved the assembly in some plasmids as did prior enrichment of plasmids. While cp32 plasmids remained refractory to assembly using only short reads they were effectively assembled by long read sequencing methods. The long read SMRT and nanopore sequences came, however, at the cost of indels (insertions or deletions) appearing in an unpredictable manner. Using long and short read technologies together allowed us to show that the three B. burgdorferi s.s. strains investigated here, whilst having similar plasmid structures to each other (apart from fusion of cp32 plasmids), differed significantly from the reference strain B31-GB, especially in the case of cp32 plasmids.ConclusionShort read methods are sufficient to assemble the main chromosome and many of the plasmids in B. burgdorferi. However, a combination of short and long read sequencing methods is essential for proper assembly of all plasmids including cp32 and thus, for gaining an understanding of host- or vector adaptations. An important conclusion from our work is that the evolution of Borrelia plasmids appears to be dynamic. This has important implications for the development of useful research strategies to monitor the risk of Lyme disease occurrence and how to medically manage it.